@gmod/bam 8.9.0 → 8.11.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +92 -38
- package/dist/bamFile.d.ts +4 -4
- package/dist/bamFile.js +8 -14
- package/dist/bamFile.js.map +1 -1
- package/dist/htsget.js +2 -35
- package/dist/htsget.js.map +1 -1
- package/dist/index.d.ts +4 -0
- package/dist/index.js +6 -1
- package/dist/index.js.map +1 -1
- package/dist/streamBam.d.ts +101 -0
- package/dist/streamBam.js +227 -0
- package/dist/streamBam.js.map +1 -0
- package/dist/util.d.ts +4 -0
- package/dist/util.js +9 -1
- package/dist/util.js.map +1 -1
- package/esm/bamFile.d.ts +4 -4
- package/esm/bamFile.js +3 -9
- package/esm/bamFile.js.map +1 -1
- package/esm/htsget.js +2 -2
- package/esm/htsget.js.map +1 -1
- package/esm/index.d.ts +4 -0
- package/esm/index.js +4 -0
- package/esm/index.js.map +1 -1
- package/esm/streamBam.d.ts +101 -0
- package/esm/streamBam.js +221 -0
- package/esm/streamBam.js.map +1 -0
- package/esm/util.d.ts +4 -0
- package/esm/util.js +7 -0
- package/esm/util.js.map +1 -1
- package/package.json +1 -1
- package/src/bamFile.ts +8 -19
- package/src/htsget.ts +7 -2
- package/src/index.ts +11 -0
- package/src/streamBam.ts +344 -0
- package/src/util.ts +17 -0
package/README.md
CHANGED
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@@ -1,3 +1,5 @@
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# @gmod/bam
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[](https://npmjs.org/package/@gmod/bam)
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@@ -20,9 +22,10 @@ const bam = new BamFile({ bamPath: 'test.bam' })
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const records = await bam.getRecordsForRange('ctgA', 0, 50000)
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```
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Coordinates are 0-based half-open
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`
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generic-filehandle2
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Coordinates are 0-based half-open, where `samtools view` takes 1-based closed —
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`ctgA:1-50000` there is `('ctgA', 0, 50000)` here. `bamPath` reads a local file,
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so it is node-only; in the browser pass a URL or a generic-filehandle2
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filehandle instead:
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```typescript
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const bam = new BamFile({
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})
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```
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Records come back unfiltered, and
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Records come back unfiltered, and overlapping queries share them — treat them as
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read-only. Filter them yourself with the flag helpers and `getTag`, which
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decodes one tag instead of all of them:
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```typescript
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const records = (await bam.getRecordsForRange('chr1', 0, 100000)).filter(
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)
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```
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## Unsorted BAM
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A BAM that is unsorted, or still name-sorted as it came off the sequencer, has
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no index to query and so no `chr:start-end` to query it with. `streamBamRecords`
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walks one end to end instead, a batch of records at a time:
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```typescript
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import { streamBamRecords } from '@gmod/bam'
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for await (const records of streamBamRecords({ bamUrl: 'unsorted.bam' })) {
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for (const record of records) {
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// ...
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}
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}
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```
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It reads the file a window at a time rather than all at once, so a 1GB BAM
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streams through in bounded memory. A standalone function rather than a `BamFile`
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method, so that streaming alone leaves `BAI`/`CSI` and the chunk cache out of
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your bundle. See [docs/api.md](docs/api.md) for `onHeader` and the window size.
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## Mismatches
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`record.getMismatches()` gives every difference between a read and the reference
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— substitutions, insertions, deletions, reference skips and clips — without you
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`record.forEachMismatch(cb, opts?)`, which allocates nothing per difference and
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takes a reference window to report within.
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Substitutions need either an `MD` tag on the read or the reference bases, and
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most aligners leave `MD` off. `fetchReferenceSequence` is how you supply them:
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interpreting `CIGAR` and `MD` yourself:
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```typescript
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const bam = new BamFile({
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bamPath: 'test.bam',
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-
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// reference bases for reads with no MD tag, at most one call per query
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fetchReferenceSequence: (refName, start, end) =>
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myGenome.getSequence(refName, start, end),
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})
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for (const record of await bam.getRecordsForRange('ctgA', 0, 50000)) {
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// for a read at 100 with CIGAR 5M1I4M2D3M, SEQ ACGGTCAACGTTA, MD 3A5^GG3
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for (const { code, refPos, length, bases } of record.getMismatches()) {
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console.log(String.fromCharCode(code), refPos, length, bases)
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}
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}
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// X 103 1 G substitution to G, over a reference A
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// I 105 0 C one base inserted before 105
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// D 109 2 two reference bases deleted from 109
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```
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`code` is a CIGAR char code, to compare against the exported `MISMATCH_SUBST`,
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`MISMATCH_INSERTION`, … constants, and `record.forEachMismatch(cb, opts?)`
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reports the same set while allocating nothing per difference. What those two
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fields say, with that read walked through them:
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[docs/cigar-and-md.md](docs/cigar-and-md.md).
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Substitutions need either an `MD` tag on the read or the reference bases, which
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is what `fetchReferenceSequence` is doing above — most aligners leave `MD` off,
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and a query calls it only when one of its reads needs it. Without it, a read
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lacking `MD` still reports its indels and clips but no substitutions — nothing
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in the record says where they are. [docs/api.md](docs/api.md#mismatches) has the
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field meanings, and what to do about reads that run past the region you are
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looking at.
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## How a query flows
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A query turns the region into BGZF chunks through the index and decompresses
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each one in wasm. With nothing cached yet, decompression takes 70-90% of the
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time that query needs. The rest is ordinary JS: records are views into their
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chunk's decompressed buffer, and their fields decode on access, so a query costs
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what you read off it. [docs/dataflow.md](docs/dataflow.md) has the diagram and
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walks it through.
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The file then holds on to those decompressed chunks, so overlapping and adjacent
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queries reuse them instead of inflating again — up to 1GB per file, dropped
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after three idle minutes. A consumer holding one file per track should bound
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them together with a shared `cacheBudget` rather than shrinking each file's own
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ceiling: [docs/caching.md](docs/caching.md).
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## Decompressing on a worker pool
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BGZF
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[`@gmod/bgzf-filehandle`](https://github.com/GMOD/bgzf-filehandle) worker pool
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and it inflates chunks there instead of on the calling thread — measured
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2.7-4.1x on the pool's own fixtures.
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BGZF blocks inflate independently, so that decompression can spread across
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threads — measured 2.7-4.1x on the pool's own fixtures.
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```typescript
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import { getSharedWorkerPool } from '@gmod/bgzf-filehandle'
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})
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```
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lifecycle and the pool's own benchmarks, see
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Safe to pass unconditionally: `getSharedWorkerPool()` returns `undefined` under
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node, or anywhere the host forbids Workers, which keeps the in-process path. No
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cross-origin isolation needed. bam-js never creates a pool on its own — the
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thread budget belongs to the consumer. Worker counts, lifecycle and benchmarks:
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[bgzf-filehandle's worker pool docs](https://github.com/GMOD/bgzf-filehandle/blob/main/docs/worker-pool.md).
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## Usage with htsget
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const records = await bam.getRecordsForRange('1', 2000000, 2000001)
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```
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htsget fetches the server's range as-is, so
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`fetch` that adds the bearer token:
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htsget fetches the server's range as-is, so it ignores the mate-pairing options.
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Pass a `fetch` to add auth:
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```typescript
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const bam = new HtsgetFile({
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})
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```
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That `fetch` serves the ticket request _and_ the data-block urls the ticket
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points at, which may live on a third-party host — so only attach credentials to
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hosts you trust.
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## Docs
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- [docs/api.md](docs/api.md) — every constructor option, method and `BamRecord`
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field, plus custom record classes
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- [docs/cigar-and-md.md](docs/cigar-and-md.md) — what `CIGAR` and `MD` say, and
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how the walk reads mismatches out of them
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- [docs/dataflow.md](docs/dataflow.md) — how a query flows, and where wasm sits
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- [docs/optimizations.md](docs/optimizations.md) — why each step of that path
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looks the way it does, and what measured it
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- [docs/caching.md](docs/caching.md) — sizing the parsed-chunk cache
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- [agent-docs/adr/](agent-docs/adr/) — the measurements behind the performance
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and caching decisions
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- [CONTRIBUTING.md](CONTRIBUTING.md) — development and release steps
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## Academic Use
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Written with [NHGRI](http://genome.gov) funding as part of
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[JBrowse](http://jbrowse.org). If you use this in a publication, please cite the
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most recent JBrowse paper at [jbrowse.org](http://jbrowse.org).
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## License
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MIT © [Colin Diesh](https://github.com/cmdcolin)
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package/dist/bamFile.d.ts
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*/
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export type ReferenceSequenceFetcher = (refName: string, start: number, end: number, opts?: BaseOpts) => Promise<string>;
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export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (byteArray: Uint8Array, start: number, end: number, fileOffset: number, dataView: DataView) => T;
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export declare const BAM_MAGIC = 21840194;
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interface ChunkEntry<T> {
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bytes: number;
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features: T[];
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* A `@gmod/bgzf-filehandle` worker pool to inflate this file's chunks on,
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* instead of inflating them on the calling thread.
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* BGZF
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* Inflating the BGZF blocks is 70-90% of the wall clock of a query that
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* finds nothing cached (ADR 0003), and BGZF blocks are independently
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* inflatable, so this is the one remaining lever of that size. Measured
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* 2.7-4.1x on the pool's own fixtures.
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* so a caller whose own construction is synchronous can hand the pending
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package/dist/bamFile.js
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exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS = exports.DEFAULT_MAX_CACHE_BYTES =
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exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS = exports.DEFAULT_MAX_CACHE_BYTES = void 0;
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const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
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const shared_read_cache_1 = require("@gmod/shared-read-cache");
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const crc32_1 = __importDefault(require("crc/calculators/crc32"));
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const generic_filehandle2_1 = require("generic-filehandle2");
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const bai_ts_1 = __importDefault(require("./bai.js"));
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const csi_ts_1 = __importDefault(require("./csi.js"));
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const nullFilehandle_ts_1 = __importDefault(require("./nullFilehandle.js"));
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const reference_ts_1 = require("./reference.js");
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const sam_ts_1 = require("./sam.js");
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exports.BAM_MAGIC = 21840194;
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const blockLen = 1 << 16;
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// Ceiling on GROWING the header read. A million contigs is roughly 10MB of
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// compressed @SQ lines and ref-seq table, so a read that has doubled past this
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// than a guess, so a header that genuinely runs past this still gets its one
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// exact read. See getHeaderPre.
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const maxHeaderReadLen = 32 * 1024 * 1024;
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function resolveFilehandle(filehandle, path, url) {
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return (filehandle ??
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(path ? new generic_filehandle2_1.LocalFile(path) : url ? new generic_filehandle2_1.RemoteFile(url) : undefined));
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}
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/**
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* Whether a chunk's first record already lies past `chrId:..-max`, which means
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* every later chunk does too and none of them need to be read.
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cacheKey: chunkCacheKey,
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fill: (chunk, signal) => this._readChunkFeatures(chunk, { signal }),
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});
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const bamFh = resolveFilehandle(bamFilehandle, bamPath, bamUrl);
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const bamFh = (0, util_ts_1.resolveFilehandle)(bamFilehandle, bamPath, bamUrl);
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if (bamFh) {
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this.bam = bamFh;
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}
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else {
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throw new Error('no bam source: pass bamFilehandle, bamPath, bamUrl, or htsget: true');
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}
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const csiFh = resolveFilehandle(csiFilehandle, csiPath, csiUrl);
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const baiFh = resolveFilehandle(baiFilehandle, baiPath, baiUrl) ??
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|
-
resolveFilehandle(undefined, bamPath ? `${bamPath}.bai` : undefined, bamUrl ? `${bamUrl}.bai` : undefined);
|
|
139
|
+
const csiFh = (0, util_ts_1.resolveFilehandle)(csiFilehandle, csiPath, csiUrl);
|
|
140
|
+
const baiFh = (0, util_ts_1.resolveFilehandle)(baiFilehandle, baiPath, baiUrl) ??
|
|
141
|
+
(0, util_ts_1.resolveFilehandle)(undefined, bamPath ? `${bamPath}.bai` : undefined, bamUrl ? `${bamUrl}.bai` : undefined);
|
|
148
142
|
if (csiFh) {
|
|
149
143
|
this.index = new csi_ts_1.default({ filehandle: csiFh });
|
|
150
144
|
}
|
|
@@ -203,7 +197,7 @@ class BamFile {
|
|
|
203
197
|
*/
|
|
204
198
|
applyHeader(uncba) {
|
|
205
199
|
const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
|
|
206
|
-
if (dataView.getInt32(0, true) !==
|
|
200
|
+
if (dataView.getInt32(0, true) !== util_ts_1.BAM_MAGIC) {
|
|
207
201
|
throw new Error('Not a BAM file');
|
|
208
202
|
}
|
|
209
203
|
const headLen = dataView.getInt32(4, true);
|
|
@@ -584,8 +578,8 @@ class BamFile {
|
|
|
584
578
|
// does not even take an options argument, so every read under it runs to
|
|
585
579
|
// completion and arrives here with the cancellation unnoticed. Without this
|
|
586
580
|
// a fully abandoned chunk still gets inflated and decoded — measured at 6
|
|
587
|
-
// chunks for one 20kb query on out.bam — which is
|
|
588
|
-
//
|
|
581
|
+
// chunks for one 20kb query on out.bam — which is where an uncached query
|
|
582
|
+
// spends most of its time (ADR 0003), on records nobody will ever look at.
|
|
589
583
|
//
|
|
590
584
|
// Safe precisely because this is the SHARED signal, not a caller's: it
|
|
591
585
|
// fires only once every waiter has given up, so there is never a live
|
package/dist/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
package/dist/htsget.js
CHANGED
|
@@ -1,43 +1,10 @@
|
|
|
1
1
|
"use strict";
|
|
2
|
-
var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
|
|
3
|
-
if (k2 === undefined) k2 = k;
|
|
4
|
-
var desc = Object.getOwnPropertyDescriptor(m, k);
|
|
5
|
-
if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
|
|
6
|
-
desc = { enumerable: true, get: function() { return m[k]; } };
|
|
7
|
-
}
|
|
8
|
-
Object.defineProperty(o, k2, desc);
|
|
9
|
-
}) : (function(o, m, k, k2) {
|
|
10
|
-
if (k2 === undefined) k2 = k;
|
|
11
|
-
o[k2] = m[k];
|
|
12
|
-
}));
|
|
13
|
-
var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
|
|
14
|
-
Object.defineProperty(o, "default", { enumerable: true, value: v });
|
|
15
|
-
}) : function(o, v) {
|
|
16
|
-
o["default"] = v;
|
|
17
|
-
});
|
|
18
|
-
var __importStar = (this && this.__importStar) || (function () {
|
|
19
|
-
var ownKeys = function(o) {
|
|
20
|
-
ownKeys = Object.getOwnPropertyNames || function (o) {
|
|
21
|
-
var ar = [];
|
|
22
|
-
for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
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|
23
|
-
return ar;
|
|
24
|
-
};
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|
25
|
-
return ownKeys(o);
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|
26
|
-
};
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|
-
return function (mod) {
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|
28
|
-
if (mod && mod.__esModule) return mod;
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|
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|
-
var result = {};
|
|
30
|
-
if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
|
|
31
|
-
__setModuleDefault(result, mod);
|
|
32
|
-
return result;
|
|
33
|
-
};
|
|
34
|
-
})();
|
|
35
2
|
var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
36
3
|
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
37
4
|
};
|
|
38
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
39
6
|
const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
|
|
40
|
-
const bamFile_ts_1 =
|
|
7
|
+
const bamFile_ts_1 = __importDefault(require("./bamFile.js"));
|
|
41
8
|
const chunk_ts_1 = __importDefault(require("./chunk.js"));
|
|
42
9
|
const util_ts_1 = require("./util.js");
|
|
43
10
|
const virtualOffset_ts_1 = require("./virtualOffset.js");
|
|
@@ -73,7 +40,7 @@ function htsgetErrorMessage(text) {
|
|
|
73
40
|
*/
|
|
74
41
|
function recordsOffset(uncba) {
|
|
75
42
|
const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
|
|
76
|
-
if (uncba.byteLength < 8 || dataView.getInt32(0, true) !==
|
|
43
|
+
if (uncba.byteLength < 8 || dataView.getInt32(0, true) !== util_ts_1.BAM_MAGIC) {
|
|
77
44
|
return 0;
|
|
78
45
|
}
|
|
79
46
|
const refs = (0, util_ts_1.parseRefSeqs)(uncba, 8 + dataView.getInt32(4, true), n => n);
|
package/dist/htsget.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAE7C,8DAAkC;AAClC,0DAA8B;AAC9B,uCAKkB;AAClB,yDAAkD;AA2BlD,kEAAkE;AAClE,+EAA+E;AAC/E,iFAAiF;AACjF,SAAS,kBAAkB,CAAC,IAAY;IACtC,IAAI,MAAmC,CAAA;IACvC,IAAI,CAAC;QACH,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC3B,CAAC;IAAC,MAAM,CAAC;QACP,yCAAyC;IAC3C,CAAC;IACD,MAAM,GAAG,GAAG,MAAM,EAAE,MAAM,CAAA;IAC1B,OAAO,GAAG,EAAE,KAAK,KAAK,SAAS;QAC7B,CAAC,CAAC,IAAI;QACN,CAAC,CAAC,GAAG,CAAC,OAAO,KAAK,SAAS;YACzB,CAAC,CAAC,GAAG,CAAC,KAAK;YACX,CAAC,CAAC,GAAG,GAAG,CAAC,KAAK,KAAK,GAAG,CAAC,OAAO,EAAE,CAAA;AACtC,CAAC;AAED;;;;;;;;;;;GAWG;AACH,SAAS,aAAa,CAAC,KAAiB;IACtC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;IACD,IAAI,KAAK,CAAC,UAAU,GAAG,CAAC,IAAI,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,mBAAS,EAAE,CAAC;QACrE,OAAO,CAAC,CAAA;IACV,CAAC;IACD,MAAM,IAAI,GAAG,IAAA,sBAAY,EAAC,KAAK,EAAE,CAAC,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;IACxE,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,MAAM,IAAI,KAAK,CAAC,yCAAyC,CAAC,CAAA;IAC5D,CAAC;IACD,OAAO,IAAI,CAAC,GAAG,CAAA;AACjB,CAAC;AAED,KAAK,UAAU,OAAO,CAAC,OAAgB,EAAE,GAAW,EAAE,IAAkB;IACtE,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IACpC,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CACb,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,kBAAkB,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,CAAC,EAAE,CAC9E,CAAA;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,KAAK,UAAU,UAAU,CACvB,OAAgB,EAChB,EAAE,GAAG,EAAE,OAAO,EAAe,EAC7B,IAAkB;IAElB,0EAA0E;IAC1E,uDAAuD;IACvD,+CAA+C;IAC/C,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,IAAI,EAAE,CAAA;IACpD,MAAM,GAAG,GAAG,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC;QACjC,CAAC,CAAC,MAAM,OAAO,CAAC,OAAO,EAAE,GAAG,CAAC;QAC7B,CAAC,CAAC,MAAM,OAAO,CAAC,OAAO,EAAE,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IAC3D,OAAO,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;AAChD,CAAC;AAED,KAAK,UAAU,cAAc,CAC3B,OAAgB,EAChB,GAAkB,EAClB,IAAkB;IAElB,2EAA2E;IAC3E,OAAO,IAAA,0BAAgB,EACrB,MAAM,OAAO,CAAC,GAAG,CACf,GAAG,CAAC,GAAG,CAAC,KAAK,EAAC,CAAC,EAAC,EAAE,CAAC,IAAA,uBAAK,EAAC,MAAM,UAAU,CAAC,OAAO,EAAE,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAC9D,CACF,CAAA;AACH,CAAC;AAED,MAAqB,UAEnB,SAAQ,oBAAU;IACV,OAAO,CAAQ;IAEf,OAAO,CAAQ;IAEf,OAAO,CAAS;IAExB,YAAY,IAiCX;QACC,KAAK,CAAC;YACJ,MAAM,EAAE,IAAI;YACZ,WAAW,EAAE,IAAI,CAAC,WAAW;YAC7B,aAAa,EAAE,IAAI,CAAC,aAAa;YACjC,kBAAkB,EAAE,IAAI,CAAC,kBAAkB;YAC3C,sBAAsB,EAAE,IAAI,CAAC,sBAAsB;SACpD,CAAC,CAAA;QACF,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,KAAK,IAAI,CAAC,CAAC,KAAK,EAAE,IAAI,EAAE,EAAE,CAAC,KAAK,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;IACpE,CAAC;IAED;;;OAGG;IACK,KAAK,CAAC,WAAW,CAAC,KAAa,EAAE,IAAe;QACtD,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,IAAI,KAAK,EAAE,CAAA;QACtD,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,IAAI,CAAC,OAAO,EAAE,GAAG,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAA;QACtE,MAAM,MAAM,GAAiB,MAAM,GAAG,CAAC,IAAI,EAAE,CAAA;QAC7C,OAAO,cAAc,CAAC,IAAI,CAAC,OAAO,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE;YACtD,MAAM,EAAE,IAAI,EAAE,MAAM;SACrB,CAAC,CAAA;IACJ,CAAC;IAED,KAAK,CAAC,kBAAkB,CACtB,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;QAEd,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC1B,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,GAAG,CAAC,CAAA;QACpC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,WAAW,CAClC,iBAAiB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,EACzD,IAAI,CACL,CAAA;QACD,MAAM,IAAI,GAAG,IAAI,gCAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACpC,MAAM,OAAO,GAAG,IAAI,CAAC,eAAe,CAClC,KAAK,CAAC,QAAQ,CAAC,aAAa,CAAC,KAAK,CAAC,CAAC,EACpC,EAAE,EACF,EAAE,EACF,IAAI,kBAAK,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CACzB,CAAA;QACD,MAAM,MAAM,GAAG,IAAA,uBAAa,EAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;QACtD,MAAM,IAAI,CAAC,uBAAuB,CAAC,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC,CAAA;QAC5D,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,YAAY,CAAC,OAAiB,EAAE;QACpC,wEAAwE;QACxE,wDAAwD;QACxD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,yBAAyB,EAAE,IAAI,CAAC,CAAA;QACrE,MAAM,SAAS,GAAG,IAAI,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;QACzC,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,MAAM,IAAI,KAAK,CAAC,2CAA2C,CAAC,CAAA;QAC9D,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;CACF;AAzGD,6BAyGC"}
|
package/dist/index.d.ts
CHANGED
|
@@ -3,6 +3,8 @@ export { DEFAULT_CACHE_IDLE_TIMEOUT_MS, DEFAULT_MAX_CACHE_BYTES, default as BamF
|
|
|
3
3
|
export { default as CSI } from './csi.ts';
|
|
4
4
|
export { default as BamRecord } from './record.ts';
|
|
5
5
|
export { default as HtsgetFile } from './htsget.ts';
|
|
6
|
+
export { streamBamRecords } from './streamBam.ts';
|
|
7
|
+
export type { BamStreamHeader, StreamBamOptions } from './streamBam.ts';
|
|
6
8
|
export { MISMATCH_DELETION, MISMATCH_HARD_CLIP, MISMATCH_INSERTION, MISMATCH_REF_SKIP, MISMATCH_SOFT_CLIP, MISMATCH_SUBST, forEachMismatchNumeric, } from './mismatches.ts';
|
|
7
9
|
export { CHAR_CODE_FROM_NIBBLE, packReference, referenceNibble, } from './reference.ts';
|
|
8
10
|
export type { NumericCigar } from './record.ts';
|
|
@@ -11,4 +13,6 @@ export type { Mismatch, MismatchCallback, MismatchOptions, } from './mismatches.
|
|
|
11
13
|
export type { PackedReference } from './reference.ts';
|
|
12
14
|
export type { BamOpts, BaseOpts } from './util.ts';
|
|
13
15
|
export type { IndexCovEntry } from './bai.ts';
|
|
16
|
+
export type { default as Chunk } from './chunk.ts';
|
|
17
|
+
export type { Offset, OffsetCoords } from './virtualOffset.ts';
|
|
14
18
|
export type { Fetcher } from 'generic-filehandle2';
|
package/dist/index.js
CHANGED
|
@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
3
3
|
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
|
-
exports.referenceNibble = exports.packReference = exports.CHAR_CODE_FROM_NIBBLE = exports.forEachMismatchNumeric = exports.MISMATCH_SUBST = exports.MISMATCH_SOFT_CLIP = exports.MISMATCH_REF_SKIP = exports.MISMATCH_INSERTION = exports.MISMATCH_HARD_CLIP = exports.MISMATCH_DELETION = exports.HtsgetFile = exports.BamRecord = exports.CSI = exports.BamFile = exports.DEFAULT_MAX_CACHE_BYTES = exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS = exports.BAI = void 0;
|
|
6
|
+
exports.referenceNibble = exports.packReference = exports.CHAR_CODE_FROM_NIBBLE = exports.forEachMismatchNumeric = exports.MISMATCH_SUBST = exports.MISMATCH_SOFT_CLIP = exports.MISMATCH_REF_SKIP = exports.MISMATCH_INSERTION = exports.MISMATCH_HARD_CLIP = exports.MISMATCH_DELETION = exports.streamBamRecords = exports.HtsgetFile = exports.BamRecord = exports.CSI = exports.BamFile = exports.DEFAULT_MAX_CACHE_BYTES = exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS = exports.BAI = void 0;
|
|
7
7
|
var bai_ts_1 = require("./bai.js");
|
|
8
8
|
Object.defineProperty(exports, "BAI", { enumerable: true, get: function () { return __importDefault(bai_ts_1).default; } });
|
|
9
9
|
var bamFile_ts_1 = require("./bamFile.js");
|
|
@@ -16,6 +16,11 @@ var record_ts_1 = require("./record.js");
|
|
|
16
16
|
Object.defineProperty(exports, "BamRecord", { enumerable: true, get: function () { return __importDefault(record_ts_1).default; } });
|
|
17
17
|
var htsget_ts_1 = require("./htsget.js");
|
|
18
18
|
Object.defineProperty(exports, "HtsgetFile", { enumerable: true, get: function () { return __importDefault(htsget_ts_1).default; } });
|
|
19
|
+
// The index-free whole-file walk, for BAMs an index cannot address. Kept out of
|
|
20
|
+
// BamFile so that streaming it does not drag BAI/CSI and the chunk cache into a
|
|
21
|
+
// consumer's bundle.
|
|
22
|
+
var streamBam_ts_1 = require("./streamBam.js");
|
|
23
|
+
Object.defineProperty(exports, "streamBamRecords", { enumerable: true, get: function () { return streamBam_ts_1.streamBamRecords; } });
|
|
19
24
|
// The mismatch walk, and the codes it reports differences as. The walk is
|
|
20
25
|
// exported alongside `record.forEachMismatch` for callers holding BAM's packed
|
|
21
26
|
// arrays without a record around them — a SAM parser, or a worker that was
|
package/dist/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,2CAIqB;AAHnB,2HAAA,6BAA6B,OAAA;AAC7B,qHAAA,uBAAuB,OAAA;AACvB,sHAAA,OAAO,OAAW;AAEpB,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,yCAAkD;AAAzC,uHAAA,OAAO,OAAa;AAC7B,yCAAmD;AAA1C,wHAAA,OAAO,OAAc;AAE9B,0EAA0E;AAC1E,+EAA+E;AAC/E,2EAA2E;AAC3E,2BAA2B;AAC3B,iDAQwB;AAPtB,kHAAA,iBAAiB,OAAA;AACjB,mHAAA,kBAAkB,OAAA;AAClB,mHAAA,kBAAkB,OAAA;AAClB,kHAAA,iBAAiB,OAAA;AACjB,mHAAA,kBAAkB,OAAA;AAClB,+GAAA,cAAc,OAAA;AACd,uHAAA,sBAAsB,OAAA;AAExB,8EAA8E;AAC9E,6EAA6E;AAC7E,oEAAoE;AACpE,+CAIuB;AAHrB,qHAAA,qBAAqB,OAAA;AACrB,6GAAA,aAAa,OAAA;AACb,+GAAA,eAAe,OAAA"}
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,2CAIqB;AAHnB,2HAAA,6BAA6B,OAAA;AAC7B,qHAAA,uBAAuB,OAAA;AACvB,sHAAA,OAAO,OAAW;AAEpB,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,yCAAkD;AAAzC,uHAAA,OAAO,OAAa;AAC7B,yCAAmD;AAA1C,wHAAA,OAAO,OAAc;AAE9B,gFAAgF;AAChF,gFAAgF;AAChF,qBAAqB;AACrB,+CAAiD;AAAxC,gHAAA,gBAAgB,OAAA;AAGzB,0EAA0E;AAC1E,+EAA+E;AAC/E,2EAA2E;AAC3E,2BAA2B;AAC3B,iDAQwB;AAPtB,kHAAA,iBAAiB,OAAA;AACjB,mHAAA,kBAAkB,OAAA;AAClB,mHAAA,kBAAkB,OAAA;AAClB,kHAAA,iBAAiB,OAAA;AACjB,mHAAA,kBAAkB,OAAA;AAClB,+GAAA,cAAc,OAAA;AACd,uHAAA,sBAAsB,OAAA;AAExB,8EAA8E;AAC9E,6EAA6E;AAC7E,oEAAoE;AACpE,+CAIuB;AAHrB,qHAAA,qBAAqB,OAAA;AACrB,6GAAA,aAAa,OAAA;AACb,+GAAA,eAAe,OAAA"}
|
|
@@ -0,0 +1,101 @@
|
|
|
1
|
+
import BAMFeature from './record.ts';
|
|
2
|
+
import { parseHeaderText } from './sam.ts';
|
|
3
|
+
import type { BamRecordClass, BamRecordLike } from './bamFile.ts';
|
|
4
|
+
import type { BgzfWorkerPool } from '@gmod/bgzf-filehandle';
|
|
5
|
+
import type { GenericFilehandle } from 'generic-filehandle2';
|
|
6
|
+
export interface BamStreamHeader {
|
|
7
|
+
/** the raw SAM header text, i.e. what `samtools view -H` prints */
|
|
8
|
+
headerText: string;
|
|
9
|
+
/** the same text parsed into `@HD`/`@SQ`/`@RG`… lines and their tags */
|
|
10
|
+
samHeader: ReturnType<typeof parseHeaderText>;
|
|
11
|
+
/** ref name to the `refId` records carry, from the binary ref-seq table */
|
|
12
|
+
chrToIndex: Record<string, number>;
|
|
13
|
+
/** the inverse, indexed by `refId` */
|
|
14
|
+
indexToChr: {
|
|
15
|
+
refName: string;
|
|
16
|
+
length: number;
|
|
17
|
+
}[];
|
|
18
|
+
}
|
|
19
|
+
export interface StreamBamOptions<T extends BamRecordLike = BAMFeature> {
|
|
20
|
+
bamFilehandle?: GenericFilehandle;
|
|
21
|
+
bamPath?: string;
|
|
22
|
+
bamUrl?: string;
|
|
23
|
+
recordClass?: BamRecordClass<T>;
|
|
24
|
+
renameRefSeqs?: (a: string) => string;
|
|
25
|
+
signal?: AbortSignal;
|
|
26
|
+
/**
|
|
27
|
+
* Fires once, before the first batch, with everything the ref-seq table and
|
|
28
|
+
* header text hold. A callback rather than a separate call, because the
|
|
29
|
+
* stream has to read the header anyway to find where the records start —
|
|
30
|
+
* making it a method would mean either reading the front of the file twice
|
|
31
|
+
* or holding state between two calls.
|
|
32
|
+
*/
|
|
33
|
+
onHeader?: (header: BamStreamHeader) => void;
|
|
34
|
+
/**
|
|
35
|
+
* Worker pool to inflate each window on, as in {@link BamFile}. Without one
|
|
36
|
+
* the whole walk inflates on the calling thread, which on a large file is
|
|
37
|
+
* long enough to be worth keeping off whichever thread draws — pass
|
|
38
|
+
* `getSharedWorkerPool()` in a browser, or run the stream in a worker.
|
|
39
|
+
*
|
|
40
|
+
* Takes the promise as readily as the pool, since `getSharedWorkerPool()`
|
|
41
|
+
* returns one and awaiting an already-settled promise costs a microtask.
|
|
42
|
+
*/
|
|
43
|
+
bgzfWorkerPool?: BgzfWorkerPool | Promise<BgzfWorkerPool | undefined>;
|
|
44
|
+
/**
|
|
45
|
+
* How many window reads to keep in flight at once. Defaults to
|
|
46
|
+
* {@link DEFAULT_READ_AHEAD}; 1 issues the next read only once the previous
|
|
47
|
+
* window has been handed to the caller.
|
|
48
|
+
*
|
|
49
|
+
* Depth is the whole point of it. One outstanding read overlaps a round trip
|
|
50
|
+
* with only the CPU spent on the window before it — 8% end to end over a
|
|
51
|
+
* local server with 20ms of latency — because the wait itself is still
|
|
52
|
+
* serial. Several outstanding turn N waits into roughly N/depth.
|
|
53
|
+
*
|
|
54
|
+
* Costs `depth` windows of compressed bytes held at once, and up to
|
|
55
|
+
* `depth - 1` wasted requests at EOF: a read's length is the only thing that
|
|
56
|
+
* says the file has ended, so the reads queued behind the last one have
|
|
57
|
+
* already gone out by the time it lands. A file that fits in a single window
|
|
58
|
+
* pays neither — the depth only opens up once a read comes back full.
|
|
59
|
+
*/
|
|
60
|
+
readAhead?: number;
|
|
61
|
+
/**
|
|
62
|
+
* Compressed bytes to read per request. The default reads ~1MB at a time,
|
|
63
|
+
* which is a reasonable HTTP request size and bounds how much sits
|
|
64
|
+
* decompressed at once (~8MB, since BGZF blocks are capped at 64KB and
|
|
65
|
+
* compress ~8x). Values below one maximum-size block are raised to it, since
|
|
66
|
+
* a window that cannot hold a whole block can never make progress.
|
|
67
|
+
*/
|
|
68
|
+
windowSize?: number;
|
|
69
|
+
}
|
|
70
|
+
/**
|
|
71
|
+
* Reads every record in a BAM, in file order, without an index.
|
|
72
|
+
*
|
|
73
|
+
* For BAMs that no index can address: unsorted, or name-sorted as they come off
|
|
74
|
+
* the sequencer. {@link BamFile} answers `chr:start-end` by seeking to the
|
|
75
|
+
* chunks an index names, which a file in neither order has none of.
|
|
76
|
+
*
|
|
77
|
+
* Yields records a batch at a time, one batch per window read, rather than one
|
|
78
|
+
* record per `yield`. A whole-file walk over a 1GB BAM is tens of millions of
|
|
79
|
+
* records, and an async generator pays a promise per yield — batching moves
|
|
80
|
+
* that cost to once per few thousand records and lets the caller's inner loop
|
|
81
|
+
* be synchronous:
|
|
82
|
+
*
|
|
83
|
+
* ```js
|
|
84
|
+
* for await (const records of streamBamRecords({ bamPath: 'reads.bam' })) {
|
|
85
|
+
* for (const record of records) {
|
|
86
|
+
* // ...
|
|
87
|
+
* }
|
|
88
|
+
* }
|
|
89
|
+
* ```
|
|
90
|
+
*
|
|
91
|
+
* Deliberately a standalone function and not a `BamFile` method: it shares the
|
|
92
|
+
* record parser and header parser but none of the index, chunk or cache
|
|
93
|
+
* machinery, so a consumer who only streams does not pay for `BAI`/`CSI` in
|
|
94
|
+
* their bundle.
|
|
95
|
+
*
|
|
96
|
+
* Records are views into the window they were decompressed from, as everywhere
|
|
97
|
+
* else in this library. Holding one record from a batch retains that whole
|
|
98
|
+
* window (see {@link StreamBamOptions.windowSize}), so copy out the fields you
|
|
99
|
+
* want rather than keeping a sparse selection of records from a large file.
|
|
100
|
+
*/
|
|
101
|
+
export declare function streamBamRecords<T extends BamRecordLike = BAMFeature>({ bamFilehandle, bamPath, bamUrl, recordClass, renameRefSeqs, signal, onHeader, bgzfWorkerPool, windowSize, readAhead, }: StreamBamOptions<T>): AsyncGenerator<T[], void, undefined>;
|